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| == FreeSurfer VitrualBox VM Images == '''System Requirements:'''<<BR>> Tested running on hosts: Windows 10, Mac OS 11.6 (Intel Mac) with VirtualBox 6.1.30. <<BR>> VM: minimum of 8 GB free RAM from the host, i.e., apart from RAM already in use by the host OS and other applications. <<BR>> VM: minimum of 2 CPU's/cores from the host. <<BR>> Host Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. <<BR>> Host Disk Space: ~8GB for virtual image download (compressed *.ova file), ~30G for expanded VM image. <<BR>> Host: A working network connection. |
~+Home page for the '''Virtual Course''' is [[VirtualCourse|here]]+~ |
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| '''Suggested Experience Level:'''<<BR>> Some familiarity with downloading files, e.g., via a web browser or using commands such as wget, curl from the linux terminal. <<BR>> Some familiarity with the linux terminal running bash shell including removing, copying, editing files and setting/unsetting environment variables. <<BR>> Some familiarity with simple bash commands/scripting, e.g., as found in the shell initialization file. | == Running FreeSurfer in VirtualBox 7.X == |
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| '''Install VirtualBox on your Machine:'''<<BR>> '''VirtualBox install on Windows OS host:''' [[https://drive.google.com/file/d/1vbJxFUx1qiEnC2Z0nDaOtaz8_Cira9FX/view?usp=sharing|Vbox_Windows_install.pdf]]<<BR>> '''VirtualBox install on MacOS host:''' [[https://drive.google.com/file/d/11HfpKIaJ5kUhT17o6jY4Xm-rG740OiKj/view?usp=sharing|Vbox_MacOS_install.pdf]]<<BR>> '''VirtualBox install on linux OS host:''' [[https://www.virtualbox.org/wiki/Linux_Downloads|linux downloads]]<<BR>> |
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| '''Setup and Run the Virtual Image:'''<<BR>> Once VirtualBox is installed on your host machine, you can download a 7zip file containing an image with Freesurfer and its shell environment pre-installed. The currently available images are: |
'''System Requirements:''' <<BR>> Host Intel CPU: minimum of 4 CPU's/cores and 16 GB RAM. (Arm64 processors not supported, e.g., silicon macs with M1, M2, M3 processors). <<BR>> Virtualbox VM: minimum of 2 CPU's/cores and 8G RAM allocated from the host. <<BR>> Host Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers. <<BR>> Host Disk Space: ~150GB for a complete install of Ubuntu 22, freesurfer, including all downloads. <<BR>> Host: A working network connection. <<BR>> Additionally see the [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads| Freesurfer Release 7 System Requirements]]. |
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| '''Freesurfer 7.2.0 release''' in Ubuntu 18.04.06: [[https://drive.google.com/file/d/1RDIkvyt-KPGnK84fXt1q-taqHySXoCem/view?usp=sharing|FS_7_2_0_Ubuntu_18_04_06.ova.7z]] | '''Suggested Experience Level:'''<<BR>> Some familiarity with downloading files, e.g., via a web browser or using commands such as wget, curl from the linux terminal. <<BR>> Some familiarity with the linux terminal including removing, copying, editing files and setting/unsetting environment variables. <<BR>> Some familiarity with issuing commands in the bash shell. |
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| '''Decryption of the 7zip file requires a pass code which you can obtain by sending an email to the freesurfer mail list.''' Once you have received the pass code, you can right click on the FS_7_2_0_Ubuntu_18_04_06.ova.7z file and see what options you have under the choices for "Open with". If your current program choices cannot open a 7zip file and/or accept a pass code, then try one of the following utilities: '''For decryption on Windows''' try the free version of [[https://www.win-rar.com/start.html?&L=0|WinRAR]] to expand the 7zip file. <<BR>> '''For decryption on MacOS''' try the free [[https://macpaw.com/the-unarchiver|Unarchiver]] to expand the 7zip file. <<BR>> '''For decryption on linux''' try the package manager programs, e.g., yum, dnf, apt, to download and install a 7z or 7za binary. <<BR>> Decrypting and expanding the FS_7_2_0_Ubuntu_18_04_06.ova.7z will generate a new file without the .7z extension, i.e., FS_7_2_0_Ubuntu_18_04_06.ova will be created. This is the file to import directly into VirtualBox. If the archive program creates the FS_7_2_0_Ubuntu_18_04_06.ova file inside a parent subdirectory with ''the same name as the file'', then rename the subdirectory to be something different. Be aware that some archive programs may delete the original 7zip file. '''Screenshots to setup the VM were taken from VirtualBox running on MacOS and Windows''', but apart from some variations in the GUI on different hosts, the menus options are the same on MacOS, Windows and Linux. Please refer to the document: [[https://drive.google.com/file/d/159f-7OBx3yNpDKgeSBH4v10O7A0ktVAQ/view?usp=sharing|Vbox_load_image.pdf]] |
The current instructions for creating a Virtual Box VM to host the Ubuntu 22 Linux OS running freesurfer 7.4.1 can be found [[https://drive.google.com/file/d/1uNwv29fCeuMHrmTyXw94ZSuroNsPOxu-/view?usp=sharing|here]]. This includes complete instructions about how to create a general purpose Ubuntu 22 VM on your host machine which can be configured to run any Linux software compatible with Ubuntu 22. Only the last few pages of the documentation are specific to installing freesurfer and testing the basic freesurfer environment. Apart from some variations in the appearance of the Virtual Box application windows on the different hosts, the menus options are the same on MacOS, Windows and Linux host machines. |
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| This document describes how to access (share) an external drive plugged into the Windows machine in the Ubuntu VM:<<BR>> [[https://drive.google.com/file/d/1pB8drKX_R78Eis3Lw8xqvBqpcUYd7iZ7/view?usp=sharing|Vbox_Windows_mount_external_drive.pdf]] '''Example screenshot of VM up and running:''' Once the VM starts and you have added your Freesurfer license file, you can start a terminal and it should come up with the environment set to run the 7.2.0 release. {{attachment:Ubuntu_VM_720.png}} |
This document describes how to access (share) an external drive plugged into the Windows machine in the Ubuntu VM: <<BR>>[[https://drive.google.com/file/d/1pB8drKX_R78Eis3Lw8xqvBqpcUYd7iZ7/view?usp=sharing|Vbox_Windows_mount_external_drive.pdf]] |
Home page for the Virtual Course is here
Running FreeSurfer in VirtualBox 7.X
System Requirements:
Host Intel CPU: minimum of 4 CPU's/cores and 16 GB RAM. (Arm64 processors not supported, e.g., silicon macs with M1, M2, M3 processors).
Virtualbox VM: minimum of 2 CPU's/cores and 8G RAM allocated from the host.
Host Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers.
Host Disk Space: ~150GB for a complete install of Ubuntu 22, freesurfer, including all downloads.
Host: A working network connection.
Additionally see the Freesurfer Release 7 System Requirements.
Suggested Experience Level:
Some familiarity with downloading files, e.g., via a web browser or using commands such as wget, curl from the linux terminal.
Some familiarity with the linux terminal including removing, copying, editing files and setting/unsetting environment variables.
Some familiarity with issuing commands in the bash shell.
The current instructions for creating a Virtual Box VM to host the Ubuntu 22 Linux OS running freesurfer 7.4.1 can be found here. This includes complete instructions about how to create a general purpose Ubuntu 22 VM on your host machine which can be configured to run any Linux software compatible with Ubuntu 22. Only the last few pages of the documentation are specific to installing freesurfer and testing the basic freesurfer environment. Apart from some variations in the appearance of the Virtual Box application windows on the different hosts, the menus options are the same on MacOS, Windows and Linux host machines.
See this post about how to share a subdirectory from Windows inside the Ubuntu VM.
This document describes how to access (share) an external drive plugged into the Windows machine in the Ubuntu VM:
Vbox_Windows_mount_external_drive.pdf